JAKARTA — Ansyaad Mbai, the director of Indonesia’s National Counterterrorism Agency, has a genealogy of terrorism spread across his office wall. It starts in 1949, the year Dutch colonizers acknowledged Indonesia’s independence, and extends to 2011. Like a family tree, it begins with one line and gradually branches out into an increasingly complex web with names and photos of the country’s most notorious terrorists.

“It’s like a database, the framework to coordinate intelligence,” he said.

But lately the database has expanded beyond the boundaries of the chart, as smaller, more local groups with different objectives than those of their Qaeda-affiliated predecessors drive the terrorist threat.

In the 10 years since Islamic militants blew up two nightclubs on the resort island of Bali, killing 202 people, Indonesian security forces have arrested more than 700 people on suspicion of being militants and killed around 60. All the major suspects believed to have participated in the Bali attacks on Oct. 12, 2002, have been killed or imprisoned.

Analysts say operations by Detachment 88, the elite U.S.- and Australian-trained counterterrorism squad formed shortly after the Bali blasts, have helped cripple Jemaah Islamiyah, the Southeast Asian offshoot of Al Qaeda responsible for the bombings.

The discovery in 2010 of a paramilitary training camp in the Indonesian province of Aceh that brought together a number of major militant groups did further damage, inspiring a nationwide dragnet that led to the arrest and conviction of around 200 terrorism suspects, according to the International Crisis Group, a nongovernmental organization that has studied radical activity in the country.

But while the security forces’ efforts and internal rifts have left Jemaah Islamiyah weakened, some disaffected individuals and members of vigilante groups have moved to form new cells and seek new recruits.

Their goal, analysts say, remains to establish an Islamic state in Indonesia, which is a predominantly Muslim country but has a secular government. But for many the focus is also on exacting revenge against the security forces for the continuing crackdown.

The Crisis Group says many of these new groups are small and ad hoc, and while they still seek inspiration and material support from large jihadist organizations, they act independently. Rather than the major bombing campaigns of years past, they conduct “individual jihad” against local targets.

“The threat we’ve seen recently is manageable and is being managed, but it’s hard to extinguish,” said Jim Della-Giacoma, the Crisis Group’s Southeast Asia project director. “There are still individuals with such radical ideas that they want to use violence, and still groups out there thinking of Western targets.”

There have been more than a dozen terrorist plots since 2010, according to a recent Crisis Group report. In March the counterterrorism police killed five men on Bali who analysts say had been radicalized in prison. Security officials say the men were planning a series of robberies to finance a future attack on the island. The police have stepped up security in recent days after receiving intelligence of a possible attack during commemorations of the 2002 Bali bombings on Friday.

Last month, the police arrested 10 more suspects and confiscated a dozen homemade pipe bombs. Those men were alleged to have been planning an attack against the police and lawmakers, whom some radical preachers call legitimate targets because they have blocked the creation of an Islamic state.

Actual attacks since the last major blast — in 2009, when Islamists bombed the JW Marriott and Ritz-Carlton hotels in Jakarta, killing seven — have been less damaging, as in the cases of two suicide bombers last year: one struck a mosque in a police compound and the other a church, but they killed only themselves. But they have raised concerns about the apparent ease with which small groups of extremists can form.

“It’s not every mosque, every school, every preacher. In fact, it’s a small number,” said Mr. Della-Giacoma. “But there are known communities you need to watch out for.”

Analysts say radical clerics spread their message and seek recruits through book launches and study groups. Internet forums, military training camps and prisons also serve as recruitment pools.

“They’re targeting those who have no critical thinking, people searching for an identity,” said Noor Huda Ismail, head of the Institute for International Peace Building, which tries to rehabilitate people who have served prison terms on terrorism charges by finding them jobs.

Mr. Huda, who attended an Islamic boarding school founded by a radical cleric, Abu Bakar Bashir, said many hard-line groups have charismatic leaders who cite perceived injustices against Muslims to justify violence against the government or target religions they deem antagonistic to Islam or blasphemous, like the Islamic sect Ahmadiyah.

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While the police have largely been successful in recent years in stopping plots before they happen, analysts say, combating the ideologies behind them has proved more difficult.

“I think the Aceh camp bore home that they share a common view and a sense of solidarity, and it’s part of the reason they can support an underground resistance,” said Greg Barton, a political science professor at Monash University in Australia.

Most of Indonesia’s 240 million people practice a moderate form of Islam. But the blossoming of democracy after the longtime strongman Suharto stepped down from power in 1998 permitted more militant expressions of Islam. Dozens of deadly attacks occurred between 1999 and 2005, when a second bombing in Bali killed 20 people.

Security analysts say the focus now needs to be on prevention. “We need a comprehensive strategy that looks at how extremist clerics get access to vulnerable groups,” said Sidney Jones, a senior adviser at the Crisis Group.

Mr. Bashir, the radical cleric, is now serving a 15-year term for helping set up the terrorist training camp in Aceh. Still, he frequently makes statements from prison that spread through local media.

Over the past decade the government has run small programs that involve discussions between prisoners and moderate Islamic preachers and provide economic help to the families of terrorism convicts. Another, run by a group of nongovernmental organizations led by the U.S.-based Search for Common Ground, has tutored convicted terrorists in conflict management. Universities have also provided talks, films and social gatherings to draw students away from the Indonesian Islamic State, a banned movement that has recruited on campuses.

But some who have worked on these programs say they are too small in scale and lack wider government support.

“I worry that there’s a whole lot of little activities but not a real end goal in mind,” said Brian Hanley, who was the country head of Search for Common Ground in 2010, when the prison program was in operation.

Mr. Ansyaad, the anti-terrorism chief, said some Indonesian lawmakers had resisted more vigorous efforts to tackle terrorism because they did not want to be seen as meddling in religious affairs. Competition for resources among government institutions also prevents them from working together.

That could be changing. Recently the government announced plans for a national counterterrorism program that would bring together the police, Muslim organizations, civil society groups and several government bodies, including the Ministries of Education and Religion.

“This is a program to prevent our young people from being inducted into radical ideologies that could lead them to carry out acts of terrorism,” said Dewi Fortuna Anwar, part of the political affairs team at the office of Vice President Boediono, who is coordinating the effort.

Mr. Ansyaad also advocates government standards for what clerics can preach and harsher sentences for terrorism. By not coming down harder on hate speech, incitement to violence and paramilitary training, “we’ve become a hotbed for terrorism,” he said.

Talk of restricting religious activities, however, stirs concerns among some officials and clerics of a return to Suharto’s ironfisted tactics.

“We have to be sure we don’t go down the slippery slope of allowing the government to control areas it has no business controlling, i.e., religious freedom,” said Ms. Dewi. “There’s a fine line between preventing radicalism and too much state control.”

Correction: October 12, 2012

The byline on an earlier version of this article misspelled the name of the writer. She is Sara Schonhardt, not Sara Schonhart.

A version of this article appears in print on October 12, 2012, on Page A6 of the New York edition with the headline: Indonesia Seeing Increase
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